The Sport Edition has one key feature that the SR5 doesn't (and is even optional on the Limited), and that's the X-REAS suspension. Simply put, X-REAS allows the truck to adjust the firmness of the shocks on the fly, which is designed to reduce body roll when cornering. The SE also has bigger brake rotors and calipers, which are standard on the SE and the Limited. The other SE-only features are mostly cosmetic, such as the special roof rack, running boards, and the hood scoop (which is not functional). The SE also includes some interior features as standard that are optional on the SR5, which can make the SE a better value for the money.

If you didn't notice the ride difference between the SE and the SR5, or if you liked the ride of the SR5 better, then for you it just comes down to the appearance of the other SE features and the pricing.